From 7ad8fbdd5a98fda65c72974218e500062571ccb4 Mon Sep 17 00:00:00 2001 From: depristo Date: Sun, 12 Sep 2010 14:47:19 +0000 Subject: [PATCH] Moved GATKException to exceptions git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4266 348d0f76-0448-11de-a6fe-93d51630548a --- .../net/sf/picard/reference/FastaSequenceIndexBuilder.java | 2 +- java/src/org/broadinstitute/sting/alignment/Alignment.java | 2 +- .../sting/alignment/AlignmentValidationWalker.java | 2 +- java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java | 2 +- .../org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java | 2 +- .../sting/alignment/bwa/java/AlignerTestHarness.java | 2 +- .../sting/alignment/bwa/java/AlignmentMatchSequence.java | 2 +- .../broadinstitute/sting/alignment/bwa/java/BWAAlignment.java | 2 +- .../org/broadinstitute/sting/alignment/reference/bwt/BWT.java | 2 +- .../sting/alignment/reference/bwt/BWTReader.java | 2 +- .../sting/alignment/reference/bwt/BWTWriter.java | 2 +- .../broadinstitute/sting/alignment/reference/bwt/Bases.java | 2 +- .../broadinstitute/sting/alignment/reference/bwt/Counts.java | 2 +- .../sting/alignment/reference/bwt/CreateBWTFromReference.java | 2 +- .../sting/alignment/reference/bwt/SuffixArray.java | 2 +- .../sting/alignment/reference/bwt/SuffixArrayReader.java | 2 +- .../sting/alignment/reference/bwt/SuffixArrayWriter.java | 2 +- .../alignment/reference/packing/BasePackedInputStream.java | 2 +- .../alignment/reference/packing/BasePackedOutputStream.java | 2 +- .../sting/alignment/reference/packing/PackUtils.java | 2 +- .../sting/commandline/ArgumentDefinitionGroup.java | 2 +- .../broadinstitute/sting/commandline/ArgumentDefinitions.java | 2 +- .../org/broadinstitute/sting/commandline/ArgumentIOType.java | 2 +- .../org/broadinstitute/sting/commandline/ArgumentSource.java | 2 +- .../sting/commandline/ArgumentTypeDescriptor.java | 2 +- .../broadinstitute/sting/commandline/CommandLineUtils.java | 2 +- .../org/broadinstitute/sting/commandline/ParsingEngine.java | 2 +- .../org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 1 + java/src/org/broadinstitute/sting/gatk/ReadMetrics.java | 2 +- java/src/org/broadinstitute/sting/gatk/WalkerManager.java | 2 +- .../sting/gatk/arguments/GATKArgumentCollection.java | 2 +- .../broadinstitute/sting/gatk/contexts/AlignmentContext.java | 2 +- .../broadinstitute/sting/gatk/contexts/ReferenceContext.java | 2 +- .../sting/gatk/contexts/StratifiedAlignmentContext.java | 2 +- .../gatk/contexts/variantcontext/VariantContextUtils.java | 1 + .../sting/gatk/datasources/DataSourceGenerationException.java | 2 +- .../sting/gatk/datasources/providers/LocusReferenceView.java | 2 +- .../sting/gatk/datasources/providers/ReferenceView.java | 3 +-- .../sting/gatk/datasources/providers/ShardDataProvider.java | 2 +- .../sting/gatk/datasources/shards/IntervalSharder.java | 1 + .../sting/gatk/datasources/shards/MonolithicShard.java | 2 +- .../sting/gatk/datasources/shards/ShardStrategyFactory.java | 2 +- .../datasources/simpleDataSources/ReferenceDataSource.java | 2 +- .../simpleDataSources/ReferenceOrderedDataSource.java | 2 +- .../gatk/datasources/simpleDataSources/ResourcePool.java | 2 +- .../gatk/datasources/simpleDataSources/SAMDataSource.java | 2 +- .../simpleDataSources/SimpleDataSourceLoadException.java | 2 +- .../simpleDataSources/SimpleDataSourceSplitException.java | 2 +- .../sting/gatk/datasources/utilities/BAMFileStat.java | 2 +- .../org/broadinstitute/sting/gatk/executive/Accumulator.java | 2 +- .../sting/gatk/executive/HierarchicalMicroScheduler.java | 2 +- .../broadinstitute/sting/gatk/executive/ShardTraverser.java | 2 +- .../org/broadinstitute/sting/gatk/executive/TreeReducer.java | 2 +- java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java | 2 +- .../sting/gatk/io/storage/OutputStreamStorage.java | 2 +- .../broadinstitute/sting/gatk/io/storage/StorageFactory.java | 2 +- .../sting/gatk/io/storage/VCFWriterStorage.java | 2 +- .../broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java | 2 +- .../sting/gatk/iterators/BufferingReadIterator.java | 2 +- .../broadinstitute/sting/gatk/phonehome/GATKRunReport.java | 2 +- .../org/broadinstitute/sting/gatk/refdata/IntervalRod.java | 2 +- java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java | 2 +- .../broadinstitute/sting/gatk/refdata/RODRecordIterator.java | 2 +- .../broadinstitute/sting/gatk/refdata/RODRecordListImpl.java | 2 +- .../broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java | 2 +- .../sting/gatk/refdata/SeekableRODIterator.java | 2 +- .../sting/gatk/refdata/features/refseq/RefSeqFeature.java | 2 +- .../sting/gatk/refdata/tracks/RMDTrackCreationException.java | 2 +- .../sting/gatk/refdata/tracks/TribbleTrack.java | 2 +- .../gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java | 2 +- .../gatk/walkers/analyzeannotations/AnnotationDatum.java | 2 +- .../sting/gatk/walkers/annotator/HaplotypeScore.java | 2 +- .../sting/gatk/walkers/annotator/VariantAnnotatorEngine.java | 2 +- .../gatk/walkers/annotator/genomicannotator/JoinTable.java | 2 +- .../walkers/annotator/genomicannotator/JoinTableParser.java | 2 +- .../annotator/genomicannotator/TranscriptToGenomicInfo.java | 2 +- .../sting/gatk/walkers/coverage/CoverageUtils.java | 2 +- .../sting/gatk/walkers/coverage/DepthOfCoverageWalker.java | 1 + .../sting/gatk/walkers/fasta/FastaSequence.java | 2 +- .../sting/gatk/walkers/filters/FiltrationContextWindow.java | 4 ++-- .../walkers/genotyper/DiploidGenotypeCalculationModel.java | 1 + .../gatk/walkers/genotyper/SimpleIndelCalculationModel.java | 1 + .../sting/gatk/walkers/indels/IndelRealigner.java | 1 + .../sting/gatk/walkers/qc/CycleQualityWalker.java | 2 +- .../sting/gatk/walkers/qc/ReadValidationWalker.java | 2 +- .../sting/gatk/walkers/qc/ValidatingPileupWalker.java | 1 + .../sting/gatk/walkers/recalibration/RecalDataManager.java | 1 + .../sting/gatk/walkers/varianteval/CountVariants.java | 2 +- .../sting/gatk/walkers/varianteval/GenotypeConcordance.java | 2 +- .../sting/gatk/walkers/varianteval/IndelLengthHistogram.java | 2 +- .../gatk/walkers/varianteval/MendelianViolationEvaluator.java | 2 +- .../sting/gatk/walkers/varianteval/SimpleMetricsByAC.java | 2 +- .../sting/gatk/walkers/varianteval/VariantEvalWalker.java | 2 +- .../variantrecalibration/VariantGaussianMixtureModel.java | 2 +- .../oneoffprojects/walkers/BeagleOutputByDepthWalker.java | 2 +- .../oneoffprojects/walkers/DesignFileGeneratorWalker.java | 2 +- .../oneoffprojects/walkers/DownsamplingValidationWalker.java | 2 +- .../oneoffprojects/walkers/MendelianViolationClassifier.java | 1 + .../oneoffprojects/walkers/QualityScoreByStrandWalker.java | 2 +- .../sting/oneoffprojects/walkers/TestReadFishingWalker.java | 2 +- .../sting/oneoffprojects/walkers/VCF4WriterTestWalker.java | 2 +- .../playground/analyzeconcordance/AnalyzeConcordance.java | 2 +- .../sting/playground/examples/SampleXmlMarshaller.java | 2 +- .../sting/playground/gatk/walkers/LocusMismatchWalker.java | 2 +- .../playground/gatk/walkers/ReadBackedPhasingWalker.java | 1 + .../walkers/hybridselection/CoverageAcrossBaitsWalker.java | 2 +- .../sting/playground/gatk/walkers/phasing/Biallele.java | 2 +- .../sting/playground/gatk/walkers/phasing/BialleleSNP.java | 2 +- .../gatk/walkers/validation/RodSystemValidationWalker.java | 2 +- .../org/broadinstitute/sting/playground/utils/GenomicMap.java | 1 + .../broadinstitute/sting/playground/utils/ProcessUtils.java | 2 +- .../sting/playground/utils/report/AnalysisModuleScanner.java | 2 +- .../sting/playground/utils/report/ReportMarshaller.java | 2 +- .../sting/queue/extensions/gatk/GATKExtensionsGenerator.java | 2 +- .../org/broadinstitute/sting/utils/CardinalityCounter.java | 2 ++ java/src/org/broadinstitute/sting/utils/GenomeLoc.java | 1 + java/src/org/broadinstitute/sting/utils/GenomeLocParser.java | 1 + .../org/broadinstitute/sting/utils/GenomeLocSortedSet.java | 1 + java/src/org/broadinstitute/sting/utils/HeapSizeMonitor.java | 2 ++ .../sting/utils/MalformedGenomeLocException.java | 2 ++ java/src/org/broadinstitute/sting/utils/PathUtils.java | 2 ++ .../org/broadinstitute/sting/utils/ReservoirDownsampler.java | 2 +- .../broadinstitute/sting/utils/SequenceDictionaryUtils.java | 1 + java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java | 1 + .../org/broadinstitute/sting/utils/classloader/JVMUtils.java | 2 +- .../broadinstitute/sting/utils/classloader/PackageUtils.java | 2 +- .../broadinstitute/sting/utils/classloader/PluginManager.java | 2 +- .../broadinstitute/sting/utils/collections/CircularArray.java | 2 +- .../sting/utils/collections/MergingIterator.java | 2 +- .../org/broadinstitute/sting/utils/duplicates/DupUtils.java | 1 + .../sting/utils/{ => exceptions}/GATKException.java | 2 +- .../broadinstitute/sting/utils/exceptions/UserException.java | 1 - .../sting/utils/fasta/ArtificialFastaUtils.java | 2 +- .../org/broadinstitute/sting/utils/file/FSLockWithShared.java | 2 +- .../broadinstitute/sting/utils/genotype/LikelihoodObject.java | 2 +- .../broadinstitute/sting/utils/genotype/glf/GLFReader.java | 2 +- .../broadinstitute/sting/utils/genotype/glf/GLFRecord.java | 2 +- .../broadinstitute/sting/utils/help/ApplicationDetails.java | 2 +- .../sting/utils/help/ResourceBundleExtractorDoclet.java | 2 +- .../broadinstitute/sting/utils/instrumentation/Sizeof.java | 2 +- .../sting/utils/pileup/AbstractReadBackedPileup.java | 2 +- .../sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java | 2 +- .../org/broadinstitute/sting/utils/sam/AlignmentUtils.java | 2 +- .../sting/utils/sam/ArtificialSAMFileReader.java | 2 +- .../sting/utils/sam/ArtificialSAMQueryIterator.java | 2 +- .../broadinstitute/sting/utils/sam/ArtificialSAMUtils.java | 2 +- .../broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java | 2 +- .../broadinstitute/sting/utils/text/TextFormattingUtils.java | 2 +- .../org/broadinstitute/sting/utils/wiggle/WiggleWriter.java | 2 +- java/test/org/broadinstitute/sting/BaseTest.java | 2 +- java/test/org/broadinstitute/sting/WalkerTest.java | 2 +- .../sting/commandline/ParsingEngineUnitTest.java | 2 +- .../gatk/datasources/providers/ShardDataProviderUnitTest.java | 2 +- .../sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java | 2 +- .../sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java | 2 +- .../broadinstitute/sting/utils/GenomeLocParserUnitTest.java | 1 + .../sting/utils/GenomeLocSortedSetUnitTest.java | 1 + .../org/broadinstitute/sting/utils/PathUtilsUnitTest.java | 1 + .../sting/utils/genotype/vcf/VCFWriterUnitTest.java | 2 +- .../utils/interval/IntervalFileMergingIteratorUnitTest.java | 4 +--- 160 files changed, 164 insertions(+), 139 deletions(-) rename java/src/org/broadinstitute/sting/utils/{ => exceptions}/GATKException.java (96%) diff --git a/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java b/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java index 2bfea3c23..0244434b4 100644 --- a/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java +++ b/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java @@ -26,7 +26,7 @@ package net.sf.picard.reference; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceDataSourceProgressListener; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import static net.sf.picard.reference.FastaSequenceIndexBuilder.Status.*; diff --git a/java/src/org/broadinstitute/sting/alignment/Alignment.java b/java/src/org/broadinstitute/sting/alignment/Alignment.java index 6fa1cb1c4..98a8ed9c1 100644 --- a/java/src/org/broadinstitute/sting/alignment/Alignment.java +++ b/java/src/org/broadinstitute/sting/alignment/Alignment.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.alignment; import net.sf.samtools.*; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; diff --git a/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java index 9a0545c02..f6a40ec9d 100644 --- a/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java +++ b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java @@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.alignment.bwa.c.BWACAligner; import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java b/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java index ade0856e0..0dacfb460 100644 --- a/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java +++ b/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.bwa; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.alignment.reference.packing.PackUtils; import org.broadinstitute.sting.alignment.reference.bwt.BWT; diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java b/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java index 75207f474..8c9fba53e 100644 --- a/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java +++ b/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.alignment.bwa.c; import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMFileHeader; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; import org.broadinstitute.sting.alignment.bwa.BWTFiles; diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java index 44f9894d7..633d281a6 100644 --- a/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java +++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.alignment.bwa.java; import org.broadinstitute.sting.alignment.Aligner; import org.broadinstitute.sting.alignment.Alignment; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.BaseUtils; import java.io.File; diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java index 8f32b20cd..503b406a6 100644 --- a/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java +++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.bwa.java; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.Deque; import java.util.ArrayDeque; diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java index 8129b4dac..e86ea858e 100644 --- a/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java +++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.alignment.bwa.java; import org.broadinstitute.sting.alignment.Alignment; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import net.sf.samtools.Cigar; /** diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java index c47642faa..96ec794ce 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.alignment.reference.bwt; import org.broadinstitute.sting.alignment.reference.packing.PackUtils; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; /** * Represents the Burrows-Wheeler Transform of a reference sequence. diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java index 7ec3da734..b4e095433 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream; import org.broadinstitute.sting.alignment.reference.packing.BasePackedInputStream; import org.broadinstitute.sting.alignment.reference.packing.PackUtils; diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java index 901e1878a..f8f7782ac 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream; import org.broadinstitute.sting.alignment.reference.packing.BasePackedOutputStream; diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java index 86653912f..1a1e5e3ca 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java index 31868a165..fc06f4136 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.HashMap; import java.util.Map; diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java index a5f99792d..a78e8633b 100755 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java @@ -31,7 +31,7 @@ import net.sf.picard.reference.ReferenceSequence; import java.io.*; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.alignment.reference.packing.PackUtils; /** diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java index 4344a31b0..48868895d 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.Comparator; import java.util.TreeSet; diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java index 17ded2297..4fb983a5b 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream; import org.broadinstitute.sting.alignment.reference.packing.PackUtils; diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java index da6b0d41d..febb87f8f 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream; import java.io.*; diff --git a/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java index 151fd0ebb..c3291774e 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.packing; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.io.*; import java.nio.ByteOrder; diff --git a/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java index 828ba52af..cfdb10949 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.packing; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.io.*; import java.nio.ByteBuffer; diff --git a/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java index 6ff2bf938..3ab0b7589 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.packing; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.io.File; import java.io.IOException; diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java index 58d985a2f..6ae6bc053 100644 --- a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java +++ b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.commandline; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.List; import java.util.Collections; diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java index d4b774acd..88503eacd 100755 --- a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java +++ b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.commandline; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.Set; import java.util.HashSet; diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java b/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java index 93cabf0e3..9b21def56 100644 --- a/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java +++ b/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java @@ -24,7 +24,7 @@ package org.broadinstitute.sting.commandline; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.lang.annotation.Annotation; diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java b/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java index 9fa9677c9..fedbe815c 100644 --- a/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java +++ b/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.commandline; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.lang.reflect.Field; import java.util.Arrays; diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java index 4c76e7958..8eea131e1 100644 --- a/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java +++ b/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.commandline; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.gatk.walkers.Multiplex; import org.broadinstitute.sting.gatk.walkers.Multiplexer; diff --git a/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java b/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java index 29991bc72..0fdeda438 100644 --- a/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java +++ b/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.commandline; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.walkers.Walker; diff --git a/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java b/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java index c112db695..9b8e6ad23 100755 --- a/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java +++ b/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.commandline; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.utils.Utils; diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index b1cda6547..2bcc58aac 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -31,6 +31,7 @@ import net.sf.samtools.*; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalUtils; diff --git a/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java b/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java index f9198a2ce..fdc2cb459 100755 --- a/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java +++ b/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java @@ -30,7 +30,7 @@ import java.util.Map; import java.util.HashMap; import java.util.Collections; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; /** * Holds a bunch of basic information about the traversal. diff --git a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java index 523fd4e88..18bf662eb 100755 --- a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java +++ b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java @@ -30,7 +30,7 @@ import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.gatk.filters.FilterManager; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.text.TextFormattingUtils; import org.broadinstitute.sting.utils.help.DescriptionTaglet; diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 00a076d69..d80e95462 100755 --- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.arguments; import net.sf.samtools.SAMFileReader; import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Input; diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java index 49ea45901..29867a7f4 100755 --- a/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java +++ b/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.gatk.contexts; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java index c550b04bd..0221ef3db 100644 --- a/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java +++ b/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.contexts; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.BaseUtils; import net.sf.samtools.util.StringUtil; diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java index 5893238bc..2be1dea28 100755 --- a/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java +++ b/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.contexts; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.*; diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java index 21231ed93..eb037cf09 100755 --- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java +++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java @@ -30,6 +30,7 @@ import org.broad.tribble.util.popgen.HardyWeinbergCalculation; import org.broad.tribble.util.variantcontext.*; import org.broadinstitute.sting.utils.*; import org.broad.tribble.vcf.VCFConstants; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.UserException; public class VariantContextUtils { diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java b/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java index 14e90ba95..d1c2b2b76 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.datasources; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; /** * User: aaron diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java index 2801e2b8b..83fefe700 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.gatk.walkers.Walker; diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java index 9215f5770..ee4997164 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java @@ -1,6 +1,5 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.*; import java.util.Collections; @@ -9,9 +8,9 @@ import java.util.Arrays; import net.sf.samtools.SAMSequenceRecord; import net.sf.samtools.SAMRecord; -import net.sf.samtools.util.StringUtil; import net.sf.picard.reference.ReferenceSequence; import net.sf.picard.reference.IndexedFastaSequenceFile; +import org.broadinstitute.sting.utils.exceptions.GATKException; /** * User: hanna * Date: May 22, 2009 diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java index 6df5f7a26..f4ca0b05c 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.providers; import org.broadinstitute.sting.gatk.datasources.shards.Shard; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.ArrayList; import java.util.List; diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java index b60c133d0..5f9bdb958 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java @@ -35,6 +35,7 @@ import java.util.*; import net.sf.samtools.*; import net.sf.picard.util.PeekableIterator; +import org.broadinstitute.sting.utils.exceptions.GATKException; /** * Shard intervals based on position within the BAM file. diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java index 0ec3eead2..2af2caf68 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.datasources.shards; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.gatk.ReadMetrics; import org.broadinstitute.sting.gatk.ReadProperties; diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java index db6d4d0da..74ee8361e 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.shards; import net.sf.samtools.SAMSequenceDictionary; import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource; diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java index a70123371..83d4ad469 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import net.sf.picard.reference.FastaSequenceIndexBuilder; import net.sf.picard.sam.CreateSequenceDictionary; import net.sf.picard.reference.IndexedFastaSequenceFile; diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java index 70fce919d..1aaee0bb2 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java @@ -11,7 +11,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.FlashBackIterator; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java index 2308bc5d4..862c58617 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java index 952041dd9..69d43b92a 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java @@ -41,7 +41,7 @@ import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.ReadMetrics; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.File; diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java index 4446e90d2..7dc2b51fa 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; /** * diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java index 62826007f..040327bc3 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; /* diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java b/java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java index e0448cd13..1cadb1252 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.datasources.utilities; import org.broadinstitute.sting.commandline.CommandLineProgram; import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.instrumentation.Sizeof; import java.io.File; diff --git a/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java b/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java index 1a23eb2bf..6d2a25565 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java @@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.GenomeLocSortedSet; diff --git a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java index 6e83e6b46..477d522a1 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java @@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.io.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor; import javax.management.MBeanServer; diff --git a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java index 4b1678f32..661a99fd6 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java @@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.traversals.TraversalEngine; import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.LocusWalker; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.concurrent.Callable; /** diff --git a/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java b/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java index 47b8a048a..8485eafd5 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.executive; import org.broadinstitute.sting.gatk.walkers.TreeReducible; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.concurrent.Callable; import java.util.concurrent.Future; diff --git a/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java b/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java index bb6d762fa..92bf8327b 100755 --- a/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java +++ b/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.io; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.commandline.ArgumentSource; import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder; diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java index fd47b88e7..541a46b3b 100644 --- a/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java +++ b/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.io.storage; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java b/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java index 0edeb0eb6..ffd9b8c83 100644 --- a/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java +++ b/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java @@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.io.stubs.Stub; import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub; import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub; import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.io.File; diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java index bcaee1cf8..539d74890 100644 --- a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java +++ b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java @@ -5,7 +5,7 @@ import org.broad.tribble.vcf.VCFHeader; import org.broad.tribble.vcf.VCFHeaderLine; import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.vcf.VCFWriter; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub; import java.io.*; diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java index 6af299975..2b5cc7917 100644 --- a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java +++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java @@ -35,7 +35,7 @@ import java.io.OutputStream; import org.broadinstitute.sting.gatk.io.OutputTracker; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.UserException; /** diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java index ce583ff57..f913f9464 100644 --- a/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java +++ b/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java @@ -31,7 +31,7 @@ import java.util.Queue; import java.util.LinkedList; import java.util.NoSuchElementException; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; /** * Buffers access to a large stream of reads, replenishing the buffer only when the reads diff --git a/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java index 998b69bb0..6cab3a353 100644 --- a/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java +++ b/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java @@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.Utils; import org.simpleframework.xml.Element; import org.simpleframework.xml.ElementList; diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java b/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java index e95d394f0..0b1c41857 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.refdata; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import java.io.File; diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java b/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java index e19b220b2..215c09f55 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.refdata; import org.broad.tribble.util.variantcontext.Allele; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java b/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java index 25e49aa94..5f7bd10f8 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.refdata; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.text.XReadLines; diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java b/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java index 96312d84c..e5f0487d5 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.refdata; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java index a0eea556b..a9d82a112 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java @@ -5,7 +5,7 @@ import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java b/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java index 404082354..f0180a4be 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java @@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.iterators.PushbackIterator; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java index 3a6dbd291..6e9eb88de 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java @@ -4,7 +4,7 @@ import org.broad.tribble.Feature; import org.broadinstitute.sting.gatk.refdata.Transcript; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java index 48d5af0da..484d90fdf 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java @@ -23,7 +23,7 @@ package org.broadinstitute.sting.gatk.refdata.tracks; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; /** diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/TribbleTrack.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/TribbleTrack.java index 3079a6023..9694bcb24 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/TribbleTrack.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/TribbleTrack.java @@ -30,7 +30,7 @@ import org.broad.tribble.FeatureSource; import org.broad.tribble.source.BasicFeatureSource; import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java index 3c636ff2d..56cd44aa0 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java @@ -36,7 +36,7 @@ import org.broad.tribble.util.LittleEndianOutputStream; import org.broadinstitute.sting.gatk.refdata.tracks.TribbleTrack; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java index 4f9191ed1..2995723e1 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.analyzeannotations; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.Comparator; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java index 0372eecd3..bd5406137 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java @@ -30,10 +30,10 @@ import org.broad.tribble.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.*; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.genotype.Haplotype; import org.broadinstitute.sting.utils.pileup.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index 3d0db37a7..3e49fac4a 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -49,7 +49,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.*; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.classloader.PackageUtils; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java index d1b0ded9d..fa67bf888 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java @@ -33,7 +33,7 @@ import java.util.ArrayList; import java.util.HashMap; import java.util.List; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.UserException; /** diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java index 2b603286f..c93c988a7 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java @@ -31,7 +31,7 @@ import java.util.ArrayList; import java.util.Collections; import java.util.List; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java index 1a6b3e80f..caf5f93ec 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java @@ -44,7 +44,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.UserException; /** diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java index 72be5a6ee..7eec418f9 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java @@ -4,7 +4,7 @@ import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java index 84812469d..27a95f514 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java @@ -40,6 +40,7 @@ import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.File; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java index 3e86408ef..3f3a205f9 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.fasta; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.io.PrintStream; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java index f62898643..c29711b66 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.filters; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.*; @@ -82,7 +82,7 @@ public class FiltrationContextWindow { if ( elementsToLeft > maxWindowElements() || elementsToRight > maxWindowElements() ) throw new GATKException("Too large a window requested"); if ( elementsToLeft < 0 || elementsToRight < 0 ) - throw new GATKException("Window size cannot be negative"); + throw new GATKException("Window size cannot be negative"); FiltrationContext[] array = new FiltrationContext[elementsToLeft + elementsToRight + 1]; ListIterator iter = window.listIterator(currentContext - elementsToLeft); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java index df4b19ae3..547ddde15 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java @@ -30,6 +30,7 @@ import org.broad.tribble.util.variantcontext.Genotype; import org.broad.tribble.vcf.VCFConstants; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.genotype.DiploidGenotype; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java index c93578873..e3afe847b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java @@ -5,6 +5,7 @@ import org.broad.tribble.util.variantcontext.Genotype; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.pileup.*; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.contexts.*; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 736efa908..74f025908 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -31,6 +31,7 @@ import net.sf.samtools.util.SequenceUtil; import net.sf.picard.reference.IndexedFastaSequenceFile; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalUtils; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java index 2e77ed3bb..e0b627d3d 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java @@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.collections.PrimitivePair; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.AlignmentUtils; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java index 6abdf7fef..ec3a9b677 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.qc; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMFileWriter; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java index 2bfc819dd..d06b2035d 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java @@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java index d9866fa51..2f46350a1 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java @@ -25,6 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.AlignmentUtils; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java index 173745552..a76c034ad 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java @@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.playground.utils.report.tags.Analysis; import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; @Analysis(name = "Count Variants", description = "Counts different classes of variants in the sample") diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java index 831191cfb..0a975aad0 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java @@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.playground.utils.report.tags.Analysis; import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; import org.broadinstitute.sting.playground.utils.report.utils.TableType; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java index 1b463cd6f..36edbb5dc 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java @@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.playground.utils.report.tags.Analysis; import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; import org.broadinstitute.sting.playground.utils.report.utils.TableType; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; /** * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java index 51dc5a5d2..c9b198bf1 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java @@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.playground.utils.report.tags.Analysis; import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.List; import java.util.Arrays; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java index cb840cda0..e3e88ab92 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java @@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.playground.utils.report.tags.Analysis; import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; import org.broadinstitute.sting.playground.utils.report.utils.TableType; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.ArrayList; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index a6bc8d255..76b73035a 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -45,7 +45,7 @@ import org.broadinstitute.sting.playground.utils.report.ReportMarshaller; import org.broadinstitute.sting.playground.utils.report.VE2ReportFactory; import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat; import org.broadinstitute.sting.playground.utils.report.utils.Node; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.classloader.PackageUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.commandline.Argument; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java index d8ec9547b..a7cce23ad 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.apache.log4j.Logger; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.collections.ExpandingArrayList; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java index 0774584a0..762b64e87 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java @@ -35,7 +35,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import java.io.PrintStream; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java index 33252ed58..ce24c5fc5 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java @@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.commandline.Output; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java index 23dace679..bf5d96984 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java @@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.refdata.features.samread.SAMReadFeature; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.walkers.LocusWalker; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.commandline.Argument; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java index b45f4e9a6..797a146c2 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java @@ -21,6 +21,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext; import org.broadinstitute.sting.gatk.walkers.varianteval.MendelianViolationEvaluator; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.vcf.VCFUtils; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java index 735da661a..2ead0e1e0 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers; import java.io.File; import java.io.IOException; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java index 3b949f384..6c7ab7d59 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java @@ -34,7 +34,7 @@ import org.broadinstitute.sting.alignment.bwa.c.BWACAligner; import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import net.sf.samtools.SAMRecord; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java index 043ad838c..34ab9fc64 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java @@ -11,7 +11,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrde import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.vcf.VCFUtils; diff --git a/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java b/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java index 6bbb8f0aa..e1c977501 100644 --- a/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java +++ b/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.playground.analyzeconcordance; import org.broadinstitute.sting.commandline.CommandLineProgram; import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.text.XReadLines; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.PathUtils; diff --git a/java/src/org/broadinstitute/sting/playground/examples/SampleXmlMarshaller.java b/java/src/org/broadinstitute/sting/playground/examples/SampleXmlMarshaller.java index 0699305ea..8468d87f5 100755 --- a/java/src/org/broadinstitute/sting/playground/examples/SampleXmlMarshaller.java +++ b/java/src/org/broadinstitute/sting/playground/examples/SampleXmlMarshaller.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.playground.examples; import org.apache.log4j.BasicConfigurator; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.simpleframework.xml.Element; import org.simpleframework.xml.Root; import org.simpleframework.xml.Serializer; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java index 1cb818349..2aeff6db0 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java @@ -39,7 +39,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext; import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java index 2da7acf06..433f0aecf 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java @@ -38,6 +38,7 @@ import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.vcf.VCFUtils; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java index eabc9181b..eefbd87d4 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java @@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.By; import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.LocusWalker; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.commandline.Argument; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java index 0277b4c80..7cd398031 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.phasing; import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.Genotype; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.ArrayList; import java.util.List; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java index 97d36ad0e..e5b86287a 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.phasing; import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.Genotype; import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; public class BialleleSNP extends Biallele { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java index 6ad907481..98519ccc7 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java @@ -10,7 +10,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrde import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.io.*; import java.math.BigInteger; diff --git a/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java b/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java index 0f195236c..f85f13da2 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java +++ b/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java @@ -49,6 +49,7 @@ import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.iterators.PushbackIterator; import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.collections.Pair; diff --git a/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java b/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java index 111fe5ccc..d86934baa 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java +++ b/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.playground.utils; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.text.XReadLines; import org.apache.log4j.Logger; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java b/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java index 71a6f310f..4308d93c3 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java +++ b/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.playground.utils.report; import org.broadinstitute.sting.playground.utils.report.tags.Analysis; import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; import org.broadinstitute.sting.playground.utils.report.tags.Param; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.lang.annotation.Annotation; import java.lang.reflect.Field; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java b/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java index f947e7d36..34314a4f7 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java +++ b/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.playground.utils.report; import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat; import org.broadinstitute.sting.playground.utils.report.utils.ComplexDataUtils; import org.broadinstitute.sting.playground.utils.report.utils.Node; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.io.*; import java.lang.reflect.Field; diff --git a/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java b/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java index 8d59b7665..d819c7502 100644 --- a/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java +++ b/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java @@ -39,7 +39,7 @@ import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescripto import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackManager; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.io.File; import java.io.IOException; diff --git a/java/src/org/broadinstitute/sting/utils/CardinalityCounter.java b/java/src/org/broadinstitute/sting/utils/CardinalityCounter.java index d0bdca3d0..978920d81 100644 --- a/java/src/org/broadinstitute/sting/utils/CardinalityCounter.java +++ b/java/src/org/broadinstitute/sting/utils/CardinalityCounter.java @@ -1,5 +1,7 @@ package org.broadinstitute.sting.utils; +import org.broadinstitute.sting.utils.exceptions.GATKException; + import java.util.Iterator; /** diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java index caa396bf0..93537299f 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java @@ -1,6 +1,7 @@ package org.broadinstitute.sting.utils; import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.ArrayList; import java.util.List; diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java index 9a7141086..d6530ade0 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java @@ -42,6 +42,7 @@ import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.utils.bed.BedParser; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.text.XReadLines; diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java b/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java index 5c4c4bb1c..28b4aa98c 100755 --- a/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java @@ -3,6 +3,7 @@ package org.broadinstitute.sting.utils; import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/utils/HeapSizeMonitor.java b/java/src/org/broadinstitute/sting/utils/HeapSizeMonitor.java index de0c27886..e45e883cb 100644 --- a/java/src/org/broadinstitute/sting/utils/HeapSizeMonitor.java +++ b/java/src/org/broadinstitute/sting/utils/HeapSizeMonitor.java @@ -1,5 +1,7 @@ package org.broadinstitute.sting.utils; +import org.broadinstitute.sting.utils.exceptions.GATKException; + import java.lang.management.ManagementFactory; import java.lang.management.MemoryMXBean; diff --git a/java/src/org/broadinstitute/sting/utils/MalformedGenomeLocException.java b/java/src/org/broadinstitute/sting/utils/MalformedGenomeLocException.java index d79359633..a0d11d6c7 100644 --- a/java/src/org/broadinstitute/sting/utils/MalformedGenomeLocException.java +++ b/java/src/org/broadinstitute/sting/utils/MalformedGenomeLocException.java @@ -1,4 +1,6 @@ package org.broadinstitute.sting.utils; + +import org.broadinstitute.sting.utils.exceptions.GATKException; /** * User: hanna * Date: Jun 2, 2009 diff --git a/java/src/org/broadinstitute/sting/utils/PathUtils.java b/java/src/org/broadinstitute/sting/utils/PathUtils.java index c543a29d5..2feb14484 100755 --- a/java/src/org/broadinstitute/sting/utils/PathUtils.java +++ b/java/src/org/broadinstitute/sting/utils/PathUtils.java @@ -1,5 +1,7 @@ package org.broadinstitute.sting.utils; +import org.broadinstitute.sting.utils.exceptions.GATKException; + import java.util.List; import java.util.ArrayList; import java.io.File; diff --git a/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java b/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java index 8ced0508c..b1a4e3c8d 100644 --- a/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java +++ b/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.utils; -import net.sf.picard.util.PeekableIterator; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java b/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java index 1ca720e53..4198bc9c3 100755 --- a/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java +++ b/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java @@ -29,6 +29,7 @@ import net.sf.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.UserException; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java b/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java index a88eaee09..e5819fb75 100755 --- a/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java +++ b/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java @@ -30,6 +30,7 @@ import cern.jet.random.Normal; import java.util.*; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.exceptions.GATKException; public class WilcoxonRankSum { static final String headerString = ("nA nB .005 .01 .025 .05 .10 .20"); diff --git a/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java b/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java index acb873515..905814304 100755 --- a/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java +++ b/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.classloader; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.lang.reflect.Modifier; import java.lang.reflect.Field; diff --git a/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java b/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java index c146c50f6..b97dff22c 100755 --- a/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java +++ b/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.classloader; import ch.qos.logback.classic.Level; import ch.qos.logback.classic.Logger; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import org.reflections.Reflections; import org.reflections.scanners.SubTypesScanner; diff --git a/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java b/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java index 54c33d447..4d59f9400 100644 --- a/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java +++ b/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.classloader; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import java.util.HashMap; diff --git a/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java b/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java index 93a442da8..d107b85b2 100644 --- a/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java +++ b/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.collections; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; /** This class, closely resembling a deque (except that it is not dynamically grown), diff --git a/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java b/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java index c40b1108e..c6bf96f64 100644 --- a/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java +++ b/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.collections; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java b/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java index 4403597b5..27d6619cd 100644 --- a/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java +++ b/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java @@ -28,6 +28,7 @@ package org.broadinstitute.sting.utils.duplicates; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; diff --git a/java/src/org/broadinstitute/sting/utils/GATKException.java b/java/src/org/broadinstitute/sting/utils/exceptions/GATKException.java similarity index 96% rename from java/src/org/broadinstitute/sting/utils/GATKException.java rename to java/src/org/broadinstitute/sting/utils/exceptions/GATKException.java index 291e50f39..a71cb85a8 100644 --- a/java/src/org/broadinstitute/sting/utils/GATKException.java +++ b/java/src/org/broadinstitute/sting/utils/exceptions/GATKException.java @@ -22,7 +22,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils; +package org.broadinstitute.sting.utils.exceptions; import org.broadinstitute.sting.utils.exceptions.StingException; diff --git a/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java index 4e61d7245..b7fe6655f 100755 --- a/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -28,7 +28,6 @@ import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceRecord; -import org.broadinstitute.sting.utils.GATKException; import java.io.File; import java.util.Arrays; diff --git a/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java b/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java index b6d919499..8b1e85030 100644 --- a/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java +++ b/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.utils.fasta; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.io.FileNotFoundException; import java.io.FileOutputStream; diff --git a/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java b/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java index 5ca9f0971..767a7aadf 100644 --- a/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java +++ b/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.utils.file; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.io.File; import java.io.IOException; diff --git a/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java b/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java index 6cc943fea..334394a3e 100755 --- a/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.utils.genotype; import edu.mit.broad.picard.genotype.DiploidGenotype; import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods; import net.sf.samtools.SAMFileHeader; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.HashMap; diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java index 7120d118b..bf5b15d02 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.utils.genotype.glf; import net.sf.samtools.util.BinaryCodec; import net.sf.samtools.util.BlockCompressedInputStream; import net.sf.samtools.util.RuntimeEOFException; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.genotype.LikelihoodObject; diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java index 7e481061c..5d2b8e5cf 100755 --- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.utils.genotype.glf; import net.sf.samtools.util.BinaryCodec; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; /* diff --git a/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java b/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java index cd51e3698..c2a5f8f77 100644 --- a/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java +++ b/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.help; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.commandline.CommandLineProgram; diff --git a/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java b/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java index f7760d5e7..b044f779a 100644 --- a/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java +++ b/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java @@ -31,7 +31,7 @@ import java.util.*; import java.io.PrintStream; import java.io.IOException; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.gatk.walkers.Walker; diff --git a/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java b/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java index 1b9a5009d..2eaa07d89 100644 --- a/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java +++ b/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java @@ -24,7 +24,7 @@ package org.broadinstitute.sting.utils.instrumentation; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.lang.instrument.Instrumentation; import java.lang.reflect.Field; diff --git a/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java b/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java index 4c5f9db18..7b039608f 100644 --- a/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java +++ b/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java @@ -24,7 +24,7 @@ package org.broadinstitute.sting.utils.pileup; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.gatk.iterators.IterableIterator; diff --git a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java index f873ca076..42718320e 100644 --- a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java +++ b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java @@ -23,7 +23,7 @@ */ package org.broadinstitute.sting.utils.pileup; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; diff --git a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java index d26f61596..6683c89d2 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java +++ b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java @@ -31,7 +31,7 @@ import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; import net.sf.samtools.util.StringUtil; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.pileup.*; import org.broadinstitute.sting.utils.Utils; diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java index c535b0d6d..5297e0345 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java @@ -10,7 +10,7 @@ import java.io.ByteArrayInputStream; import java.io.UnsupportedEncodingException; import java.util.*; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; /** diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java index ced8e4f4b..d98a6c6f1 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java @@ -6,7 +6,7 @@ import net.sf.samtools.SAMRecord; import java.util.List; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; /* diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java index 88696d465..b424c59a3 100755 --- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.utils.sam; import net.sf.samtools.*; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.io.File; import java.util.ArrayList; diff --git a/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java b/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java index 9e71e7836..ab22b4e19 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java +++ b/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java @@ -29,7 +29,7 @@ import net.sf.samtools.SAMFileReader; import java.io.File; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; /** * Allows the user to steadily accumulate information about what diff --git a/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java b/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java index d36617958..93cece9cd 100644 --- a/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java +++ b/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.utils.text; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import java.util.*; import java.util.regex.Pattern; diff --git a/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java b/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java index 693fe80d5..3c47d5a8b 100755 --- a/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java +++ b/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.utils.wiggle; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/test/org/broadinstitute/sting/BaseTest.java b/java/test/org/broadinstitute/sting/BaseTest.java index c7e248569..9f9f56676 100755 --- a/java/test/org/broadinstitute/sting/BaseTest.java +++ b/java/test/org/broadinstitute/sting/BaseTest.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting; import org.apache.log4j.*; import org.apache.log4j.spi.LoggingEvent; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.junit.*; import java.io.*; diff --git a/java/test/org/broadinstitute/sting/WalkerTest.java b/java/test/org/broadinstitute/sting/WalkerTest.java index 20787a14e..d82a9d76d 100755 --- a/java/test/org/broadinstitute/sting/WalkerTest.java +++ b/java/test/org/broadinstitute/sting/WalkerTest.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting; import junit.framework.Assert; import org.broadinstitute.sting.gatk.CommandLineExecutable; import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.Utils; import org.junit.Test; diff --git a/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java b/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java index c71d93902..c2650aad1 100755 --- a/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java +++ b/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.commandline; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.junit.Test; import org.junit.Before; import org.junit.Assert; diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java index 952ee4361..23decfa06 100755 --- a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.junit.Before; import org.junit.Assert; import org.junit.Test; diff --git a/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java b/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java index c4aec6c32..fb2254e6d 100644 --- a/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.filters; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.GenomeLocParser; import org.junit.BeforeClass; diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java index 7ca4fb092..98807fba0 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java @@ -27,7 +27,7 @@ import net.sf.samtools.SAMSequenceRecord; import net.sf.picard.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLocParser; import org.junit.Assert; import org.junit.Before; diff --git a/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java b/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java index 42d5b3eac..46b2ed6f2 100644 --- a/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java @@ -3,6 +3,7 @@ package org.broadinstitute.sting.utils; import net.sf.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import static org.junit.Assert.assertEquals; diff --git a/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java b/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java index 80468c720..bbb11fc86 100755 --- a/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java @@ -2,6 +2,7 @@ package org.broadinstitute.sting.utils; import net.sf.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import static org.junit.Assert.assertTrue; import static org.junit.Assert.assertEquals; diff --git a/java/test/org/broadinstitute/sting/utils/PathUtilsUnitTest.java b/java/test/org/broadinstitute/sting/utils/PathUtilsUnitTest.java index 478fed7da..f54944a05 100755 --- a/java/test/org/broadinstitute/sting/utils/PathUtilsUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/PathUtilsUnitTest.java @@ -1,6 +1,7 @@ package org.broadinstitute.sting.utils; import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.junit.BeforeClass; import org.junit.Test; import org.junit.Assert; diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java index 3f6172b07..e22b5d18a 100644 --- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java @@ -7,7 +7,7 @@ import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.vcf.*; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.refdata.tracks.builders.TribbleRMDTrackBuilder; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.junit.Assert; diff --git a/java/test/org/broadinstitute/sting/utils/interval/IntervalFileMergingIteratorUnitTest.java b/java/test/org/broadinstitute/sting/utils/interval/IntervalFileMergingIteratorUnitTest.java index b915e9222..9f94659f6 100644 --- a/java/test/org/broadinstitute/sting/utils/interval/IntervalFileMergingIteratorUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/interval/IntervalFileMergingIteratorUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.interval; -import org.broadinstitute.sting.utils.GATKException; +import org.broadinstitute.sting.utils.exceptions.GATKException; import org.junit.BeforeClass; import org.junit.Test; import org.junit.Assert; @@ -33,8 +33,6 @@ import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.StingException; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.picard.reference.ReferenceSequenceFile; import net.sf.picard.reference.ReferenceSequenceFileFactory; import java.io.File;